Bone Marrow Mononuclear Cells - Zheng et al.
Philippe Boileau
15/10/2019
Data
scRNA-seq data was captured from the bone marrow mononuclear cells of two patients with leukemia before and after undergoing a hematopoietic stem cell transplant. We subjected the cells from each patient to various dimensionality reduction techniques to determine whether they are capable of distinguishing the treatment states of the cells. scRNA-seq data from two healthy controls are used to perform cPCA and scPCA.
AML027
PCA
cPCA
scPCA
Analysis of Genes with Non-Zero Entries in Loadings Matrix
The following table provides the gene symbol and loadings of the genes with non-zero entries in one of the loadings vectors of the first two scPCs.
## # A tibble: 3 x 3
## gene_sym scPC1 scPC2
## <chr> <dbl> <dbl>
## 1 STMN1 -0.997 0
## 2 LINC00152 0.0732 0
## 3 PDLIM1 0 -1Comparison of Loadings Weights: cPCA and scPCA
The absolute valules of the loadings are not compared for this patient, since only three entries in the leading loadings vectors produced by scPCA are non-zero.
t-SNE
UMAP
ZINB-WaVE
Combined Plots
AML035
PCA
cPCA
scPCA
Analysis of Genes with Non-Zero Entries in Loadings Matrix
The following table provides the gene symbol and loadings of the genes with non-zero entries in one of the loadings vectors of the first two scPCs.
## # A tibble: 177 x 3
## gene_sym scPC1 scPC2
## <chr> <dbl> <dbl>
## 1 HBB -0.0612 0.697
## 2 HBA2 0 -0.114
## 3 HBA1 0.0957 -0.680
## 4 TMSB4X -0.000835 0
## 5 RPL10 0.0176 0
## 6 RPLP1 -0.00289 0
## 7 RPL13 -0.0317 0
## 8 RPL13A -0.0322 0
## 9 RPS4X -0.0805 0
## 10 MALAT1 0.00873 0
## # … with 167 more rowsComparison of Loadings Weights: cPCA and scPCA
t-SNE
UMAP
ZINB-WaVE
Combined Plots
